The speedy computation of eigenvalue problems is the key point in structure dynamics. In this paper, by combining transfer matrix method and finite element method, the modified finite element-transfer matrix method and its algorithm for eigenvalue problems are presented. By using this method, the speedy computation of eigenvalue problem of flexible structures can be realized, and the repeated eignvalue problem can be solved simply and conveniently. This method has the low order of system matrix, high computational efficiency, and stability. Formulations of this method, as well as some numerical examples, are given to validate the method.